trisurf-ng.git - Gitblit

Added check if trisurf executable exists in path, ETA is empty or N/A at ap...

Samo Penic

2016-05-15 38cb4ac927272256b636c014a9aec1a119958fb6

commit \| author \| age
7f6076	1	/* vim: set ts=4 sts=4 sw=4 noet : */
88f451	2	#include<math.h>
SP	3	#include<stdlib.h>
	4	#include "general.h"
	5	#include "sh.h"
267db5	6	#include "io.h"
SP	7	#include <string.h>
074a17	8
SP	9
	10	ts_spharm sph_init(ts_vertex_list vlist, ts_uint l){
eb8605	11	ts_uint j,i;
074a17	12	ts_spharm sph=(ts_spharm )malloc(sizeof(ts_spharm));
SP	13
262607	14	sph->N=0;
eb8605	15	/* lets initialize Ylm for each vertex. */
SP	16	sph->Ylmi=(ts_double *)calloc(l,sizeof(ts_double ));
5bb11d	17	for(i=0;i<l;i++){
SP	18	sph->Ylmi[i]=(ts_double *)calloc(2i+1,sizeof(ts_double *));
	19	for(j=0;j<(2*i+1);j++){
eb8605	20	sph->Ylmi[i][j]=(ts_double *)calloc(vlist->n,sizeof(ts_double));
074a17	21	}
SP	22	}
	23
	24	/* lets initialize ulm */
	25	sph->ulm=(ts_double *)calloc(l,sizeof(ts_double ));
	26	for(j=0;j<l;j++){
	27	sph->ulm[j]=(ts_double )calloc(2j+1,sizeof(ts_double));
	28	}
	29
262607	30	/* lets initialize sum of Ulm2 */
SP	31	sph->sumUlm2=(ts_double *)calloc(l,sizeof(ts_double ));
	32	for(j=0;j<l;j++){
	33	sph->sumUlm2[j]=(ts_double )calloc(2j+1,sizeof(ts_double));
	34	}
074a17	35
SP	36	/* lets initialize co */
79fc9c	37	//NOTE: C is has zero based indexing. Code is imported from fortran and to comply with original indexes we actually generate one index more. Also second dimension is 2j+2 instead of 2j+2. elements starting with 0 are useles and should be ignored!
SP	38	sph->co=(ts_double *)calloc(l+1,sizeof(ts_double ));
	39	for(j=0;j<=l;j++){
	40	sph->co[j]=(ts_double )calloc(2j+2,sizeof(ts_double));
074a17	41	}
SP	42
5bb11d	43	sph->l=l;
SP	44
	45	/* Calculate coefficients that will remain constant during all the simulation */
	46	precomputeShCoeff(sph);
	47
074a17	48	return sph;
SP	49	}
	50
	51
eb8605	52	ts_bool sph_free(ts_spharm *sph){
SP	53	int i,j;
632960	54	if(sph==NULL) return TS_FAIL;
074a17	55	for(i=0;i<sph->l;i++){
SP	56	if(sph->ulm[i]!=NULL) free(sph->ulm[i]);
262607	57	if(sph->sumUlm2[i]!=NULL) free(sph->sumUlm2[i]);
074a17	58	if(sph->co[i]!=NULL) free(sph->co[i]);
SP	59	}
79fc9c	60	if(sph->co[sph->l]!=NULL) free(sph->co[sph->l]);
074a17	61	if(sph->co != NULL) free(sph->co);
SP	62	if(sph->ulm !=NULL) free(sph->ulm);
	63
eb8605	64	if(sph->Ylmi!=NULL) {
074a17	65	for(i=0;i<sph->l;i++){
eb8605	66	if(sph->Ylmi[i]!=NULL){
5bb11d	67	for(j=0;j<i*2+1;j++){
eb8605	68	if(sph->Ylmi[i][j]!=NULL) free (sph->Ylmi[i][j]);
SP	69	}
	70	free(sph->Ylmi[i]);
	71	}
074a17	72	}
eb8605	73	free(sph->Ylmi);
074a17	74	}
eb8605	75
074a17	76	free(sph);
SP	77	return TS_SUCCESS;
	78	}
	79
88f451	80	/* Gives you legendre polynomials. Taken from NR, p. 254 */
3b3902	81	ts_double plgndr(ts_int l, ts_int m, ts_double x){
88f451	82	ts_double fact, pll, pmm, pmmp1, somx2;
SP	83	ts_int i,ll;
	84
	85	#ifdef TS_DOUBLE_DOUBLE
	86	if(m<0 \|\| m>l \|\| fabs(x)>1.0)
	87	fatal("Bad arguments in routine plgndr",1);
	88	#endif
	89	#ifdef TS_DOUBLE_FLOAT
	90	if(m<0 \|\| m>l \|\| fabsf(x)>1.0)
	91	fatal("Bad arguments in routine plgndr",1);
	92	#endif
	93	#ifdef TS_DOUBLE_LONGDOUBLE
	94	if(m<0 \|\| m>l \|\| fabsl(x)>1.0)
	95	fatal("Bad arguments in routine plgndr",1);
	96	#endif
	97	pmm=1.0;
	98	if (m>0) {
	99	#ifdef TS_DOUBLE_DOUBLE
	100	somx2=sqrt((1.0-x)*(1.0+x));
	101	#endif
	102	#ifdef TS_DOUBLE_FLOAT
	103	somx2=sqrtf((1.0-x)*(1.0+x));
	104	#endif
	105	#ifdef TS_DOUBLE_LONGDOUBLE
	106	somx2=sqrtl((1.0-x)*(1.0+x));
	107	#endif
	108	fact=1.0;
	109	for (i=1; i<=m;i++){
	110	pmm = -factsomx2;
	111	fact +=2.0;
	112	}
	113	}
	114
	115	if (l == m) return pmm;
	116	else {
	117	pmmp1=x(2m+1)*pmm;
	118	if(l==(m+1)) return(pmmp1);
	119	else {
	120	pll=0; /* so it can not be uninitialized */
	121	for(ll=m+2;ll<=l;ll++){
	122	pll=(x(2ll-1)pmmp1-(ll+m-1)pmm)/(ll-m);
	123	pmm=pmmp1;
	124	pmmp1=pll;
	125	}
	126	return(pll);
	127	}
	128	}
	129	}
	130
	131
9bf6ee	132	/** @brief: Precomputes coefficients that are required for spherical harmonics computations.
523bf1	133
9bf6ee	134	*/
523bf1	135	ts_bool precomputeShCoeff(ts_spharm *sph){
074a17	136	ts_int i,j,al,am;
SP	137	ts_double **co=sph->co;
79fc9c	138	for(i=1;i<=sph->l;i++){
SP	139	al=i;
074a17	140	sph->co[i][i+1]=sqrt((2.0*al+1.0)/2.0/M_PI);
79fc9c	141	for(j=1;j<=i-1;j++){
SP	142	am=j;
008026	143	sph->co[i][i+1+j]=co[i][i+j]*sqrt(1.0/(al-am+1.0)/(al+am));
074a17	144	sph->co[i][i+1-j]=co[i][i+1+j];
523bf1	145	}
79fc9c	146	co[i][2i+1]=co[i][2i]sqrt(1.0/(2.0al));
SP	147	co[i][1]=co[i][2*i+1];
074a17	148	co[i][i+1]=sqrt((2.0*al+1.0)/4.0/M_PI);
523bf1	149	}
SP	150	return TS_SUCCESS;
	151
	152	}
	153
	154
c9d07c	155	/** @brief: Computes Y(l,m,theta,fi)
SP	156	*
	157	* Function calculates Y^l_m for vertex with given (\theta, \fi) coordinates in
	158	* spherical coordinate system.
	159	* @param l is an ts_int argument.
	160	* @param m is an ts_int argument.
	161	* @param theta is ts_double argument.
	162	* @param fi is a ts_double argument.
	163	*
	164	* (Miha's definition that is different from common definition for factor srqt(1/(2pi)) /
88f451	165	ts_double shY(ts_int l,ts_int m,ts_double theta,ts_double fi){
SP	166	ts_double fac1, fac2, K;
	167	int i;
	168
	169	if(l<0 \|\| m>l \|\| m<-l)
	170	fatal("Error using shY function!",1);
	171
	172	fac1=1.0;
af3bad	173	for(i=1; i<=l-abs(m);i++){
88f451	174	fac1 *= i;
SP	175	}
	176	fac2=1.0;
af3bad	177	for(i=1; i<=l+abs(m);i++){
88f451	178	fac2 *= i;
SP	179	}
	180
	181	if(m==0){
	182	K=sqrt(1.0/(2.0*M_PI));
	183	}
	184	else if (m>0) {
	185	K=sqrt(1.0/(M_PI))cos(mfi);
	186	}
	187	else {
	188	//K=pow(-1.0,abs(m))sqrt(1.0/(2.0M_PI))cos(mfi);
	189	if(abs(m)%2==0)
af3bad	190	K=sqrt(1.0/(M_PI))cos(mfi);
88f451	191	else
af3bad	192	K=-sqrt(1.0/(M_PI))cos(mfi);
88f451	193	}
SP	194
632960	195	return Ksqrt((2.0l+1.0)/2.0(ts_double)(fac1/fac2))plgndr(l,abs(m),cos(theta));
88f451	196	}
523bf1	197
SP	198
	199	/* Function transforms coordinates from cartesian to spherical coordinates
	200	* (r,phi, theta). */
	201	ts_bool cart2sph(ts_coord coord, ts_double x, ts_double y, ts_double z){
	202	coord->coord_type=TS_COORD_SPHERICAL;
	203	#ifdef TS_DOUBLE_DOUBLE
	204	coord->e1=sqrt(xx+yy+z*z);
	205	if(z==0) coord->e3=M_PI/2.0;
e9c87e	206	else coord->e3=atan2(sqrt(xx+yy),z);
523bf1	207	coord->e2=atan2(y,x);
SP	208	#endif
	209	#ifdef TS_DOUBLE_FLOAT
	210	coord->e1=sqrtf(xx+yy+z*z);
	211	if(z==0) coord->e3=M_PI/2.0;
	212	else coord->e3=atanf(sqrtf(xx+yy)/z);
	213	coord->e2=atan2f(y,x);
	214	#endif
	215	#ifdef TS_DOUBLE_LONGDOUBLE
	216	coord->e1=sqrtl(xx+yy+z*z);
	217	if(z==0) coord->e3=M_PI/2.0;
	218	else coord->e3=atanl(sqrtl(xx+yy)/z);
	219	coord->e2=atan2l(y,x);
	220	#endif
	221
	222	return TS_SUCCESS;
	223	}
	224
e9c87e	225
SP	226	ts_bool sph2cart(ts_coord *coord){
	227	coord->coord_type=TS_COORD_CARTESIAN;
	228	ts_double x,y,z;
	229
	230	x=coord->e1cos(coord->e2)sin(coord->e3);
	231	y=coord->e1sin(coord->e2)sin(coord->e3);
	232	z=coord->e1*cos(coord->e3);
	233
	234	coord->e1=x;
	235	coord->e2=y;
	236	coord->e3=z;
	237
	238	return TS_SUCCESS;
	239	}
	240
	241
523bf1	242	/* Function returns radius of the sphere with the same volume as vesicle (r0) */
SP	243	ts_double getR0(ts_vesicle *vesicle){
	244	ts_double r0;
	245	#ifdef TS_DOUBLE_DOUBLE
	246	r0=pow(vesicle->volume*3.0/4.0/M_PI,1.0/3.0);
	247	#endif
	248	#ifdef TS_DOUBLE_FLOAT
	249	r0=powf(vesicle->volume*3.0/4.0/M_PI,1.0/3.0);
	250	#endif
	251	#ifdef TS_DOUBLE_LONGDOUBLE
	252	r0=powl(vesicle->volume*3.0/4.0/M_PI,1.0/3.0);
	253	#endif
	254	return r0;
	255	}
	256
	257
	258	ts_bool preparationSh(ts_vesicle *vesicle, ts_double r0){
	259	//TODO: before calling or during the call calculate area of each triangle! Can
	260	//be also done after vertexmove and bondflip //
919555	261	//DONE: in energy calculation! //
523bf1	262	ts_uint i,j;
SP	263	ts_vertex **vtx=vesicle->vlist->vtx;
	264	ts_vertex *cvtx;
	265	ts_triangle *ctri;
	266	ts_double centroid[3];
	267	ts_double r;
	268	for (i=0; i<vesicle->vlist->n; i++){
	269	cvtx=vtx[i];
	270	//cvtx->projArea=4.0M_PI/1447.0(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z)/r0/r0;
	271	cvtx->projArea=0.0;
	272
	273	/* go over all triangles that have a common vertex i */
	274	for(j=0; j<cvtx->tristar_no; j++){
	275	ctri=cvtx->tristar[j];
	276	centroid[0]=(ctri->vertex[0]->x + ctri->vertex[1]->x + ctri->vertex[2]->x)/3.0;
	277	centroid[1]=(ctri->vertex[0]->y + ctri->vertex[1]->y + ctri->vertex[2]->y)/3.0;
	278	centroid[2]=(ctri->vertex[0]->z + ctri->vertex[1]->z + ctri->vertex[2]->z)/3.0;
	279	/* calculating projArea+= area(triangle)cos(theta) /
	280	#ifdef TS_DOUBLE_DOUBLE
	281	cvtx->projArea = cvtx->projArea + ctri->area(-centroid[0]ctri->xnorm - centroid[1]ctri->ynorm - centroid[2]ctri->znorm)/ sqrt(centroid[0]centroid[0]+centroid[1]centroid[1]+centroid[2]*centroid[2]);
	282	#endif
	283	#ifdef TS_DOUBLE_FLOAT
	284	cvtx->projArea = cvtx->projArea + ctri->area(-centroid[0]ctri->xnorm - centroid[1]ctri->ynorm - centroid[2]ctri->znorm)/ sqrtf(centroid[0]centroid[0]+centroid[1]centroid[1]+centroid[2]*centroid[2]);
	285	#endif
	286	#ifdef TS_DOUBLE_LONGDOUBLE
	287	cvtx->projArea = cvtx->projArea + ctri->area(-centroid[0]ctri->xnorm - centroid[1]ctri->ynorm - centroid[2]ctri->znorm)/ sqrtl(centroid[0]centroid[0]+centroid[1]centroid[1]+centroid[2]*centroid[2]);
	288	#endif
	289	}
	290
	291	cvtx->projArea=cvtx->projArea/3.0;
	292	//we dont store spherical coordinates of vertex, so we have to calculate
	293	//r(i) at this point.
	294	#ifdef TS_DOUBLE_DOUBLE
	295	r=sqrt(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z);
	296	#endif
	297	#ifdef TS_DOUBLE_FLOAT
	298	r=sqrtf(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z);
	299	#endif
	300	#ifdef TS_DOUBLE_LONGDOUBLE
	301	r=sqrtl(cvtx->xcvtx->x+cvtx->ycvtx->y+cvtx->z*cvtx->z);
	302	#endif
	303	cvtx->relR=(r-r0)/r0;
3b3902	304	cvtx->solAngle=cvtx->projArea/r/r;
523bf1	305	}
SP	306	return TS_SUCCESS;
	307	}
	308
	309
	310
	311	ts_bool calculateYlmi(ts_vesicle *vesicle){
3b3902	312	ts_int i,j,k;
523bf1	313	ts_spharm *sph=vesicle->sphHarmonics;
SP	314	ts_coord coord=(ts_coord )malloc(sizeof(ts_coord));
	315	ts_double fi, theta;
79048f	316	ts_int m;
074a17	317	ts_vertex *cvtx;
523bf1	318	for(k=0;k<vesicle->vlist->n;k++){
074a17	319	cvtx=vesicle->vlist->vtx[k];
eb8605	320	sph->Ylmi[0][0][k]=sqrt(1.0/4.0/M_PI);
074a17	321	cart2sph(coord,cvtx->x, cvtx->y, cvtx->z);
523bf1	322	fi=coord->e2;
SP	323	theta=coord->e3;
79048f	324	for(i=1; i<sph->l; i++){
523bf1	325	for(j=0;j<i;j++){
79048f	326	m=j+1;
3b3902	327	//Nastudiraj!!!!!
79048f	328	sph->Ylmi[i][j][k]=sph->co[i][m]cos((m-i-1)fi)pow(-1,m-i-1)plgndr(i,abs(m-i-1),cos(theta));
3b3902	329	if(i==2 && j==0){
SP	330	/* fprintf(stderr," ** vtx %d **\n", k+1);
	331	fprintf(stderr,"m-i-1 =%d\n",m-i-1);
	332	fprintf(stderr,"fi =%e\n",fi);
	333	fprintf(stderr,"(m-i-1)fi =%e\n",((ts_double)(m-i-1))fi);
	334	fprintf(stderr,"-2fi =%e\n",-2fi);
	335	fprintf(stderr,"m =%d\n",m);
	336
	337	fprintf(stderr," cos(m-i-1)=%e\n",cos((m-i-1)*fi));
	338	fprintf(stderr," cos(-2fi)=%e\n",cos(-2fi));
	339	fprintf(stderr," sph->co[i][m]=%e\n",sph->co[i][m]);
	340	fprintf(stderr," plgndr(i,abs(m-i-1),cos(theta))=%e\n",plgndr(i,abs(m-i-1),cos(theta)));
	341	*/
	342	}
523bf1	343	}
3b3902	344	//Nastudiraj!!!!!
SP	345	j=i;
	346	m=j+1;
	347	sph->Ylmi[i][j][k]=sph->co[i][m]*plgndr(i,0,cos(theta));
	348	for(j=i+1;j<2*i+1;j++){
79048f	349	m=j+1;
3b3902	350	//Nastudiraj!!!!!
79048f	351	sph->Ylmi[i][j][k]=sph->co[i][m]sin((m-i-1)fi)*plgndr(i,m-i-1,cos(theta));
523bf1	352	}
SP	353	}
	354
	355	}
	356	free(coord);
	357	return TS_SUCCESS;
	358	}
	359
	360
	361
	362	ts_bool calculateUlm(ts_vesicle *vesicle){
	363	ts_uint i,j,k;
	364	ts_vertex *cvtx;
	365	for(i=0;i<vesicle->sphHarmonics->l;i++){
8e58b4	366	for(j=0;j<2*i+1;j++) vesicle->sphHarmonics->ulm[i][j]=0.0;
523bf1	367	}
SP	368
	369	//TODO: call calculateYlmi !!!
	370
	371
	372	for(k=0;k<vesicle->vlist->n; k++){
	373	cvtx=vesicle->vlist->vtx[k];
	374	for(i=0;i<vesicle->sphHarmonics->l;i++){
3b3902	375	for(j=0;j<2*i+1;j++){
eb8605	376	vesicle->sphHarmonics->ulm[i][j]+= cvtx->solAnglecvtx->relRvesicle->sphHarmonics->Ylmi[i][j][k];
523bf1	377	}
SP	378
	379	}
	380	}
	381
	382	return TS_SUCCESS;
	383	}
262607	384
SP	385
	386
	387
	388
	389	ts_bool storeUlm2(ts_vesicle *vesicle){
	390
	391	ts_spharm *sph=vesicle->sphHarmonics;
	392	ts_int i,j;
	393	for(i=0;i<sph->l;i++){
	394	for(j=0;j<2*i+1;j++){
8e58b4	395	/* DEBUG fprintf(stderr,"sph->sumUlm2[%d][%d]=%e\n",i,j,sph->ulm[i][j]* sph->ulm[i][j]); */
443ba1	396	sph->sumUlm2[i][j]+=sph->ulm[i][j]* sph->ulm[i][j];
262607	397	}
SP	398	}
	399	sph->N++;
	400	return TS_SUCCESS;
	401	}
dc77e8	402
SP	403
	404	ts_bool saveAvgUlm2(ts_vesicle *vesicle){
	405
	406	FILE *fh;
267db5	407	char filename[10000];
SP	408	strcpy(filename, command_line_args.path);
	409	strcat(filename, "sph2out.dat");
	410	fh=fopen(filename, "w");
dc77e8	411	if(fh==NULL){
SP	412	err("Cannot open file %s for writing");
	413	return TS_FAIL;
	414	}
	415
	416	ts_spharm *sph=vesicle->sphHarmonics;
	417	ts_int i,j;
	418	fprintf(fh,"l,\tm,\tulm^2avg\n");
	419	for(i=0;i<sph->l;i++){
	420	for(j=0;j<2*i+1;j++){
	421	fprintf(fh,"%d,\t%d,\t%e\n", i, j-i, sph->sumUlm2[i][j]/(ts_double)sph->N);
	422
	423	}
	424	fprintf(fh,"\n");
	425	}
	426	fclose(fh);
	427	return TS_SUCCESS;
	428	}